| Summary: | <p>Abstract</p> <p>Background</p> <p>Genetic recombination maps provide important frameworks for comparative genomics, identifying gene functions, assembling genome sequences and for breeding. The molecular recombination map currently available for the model eudicot <it>Antirrhinum majus </it>is the result of a cross with <it>Antirrhinum molle</it>, limiting its usefulness within <it>A. majus</it>.</p> <p>Results</p> <p>We created a molecular linkage map of <it>A</it>. <it>majus </it>based on segregation of markers in the F2 population of two inbred lab strains of <it>A. majus</it>. The resulting map consisted of over 300 markers in eight linkage groups, which could be aligned with a classical recombination map and the <it>A. majus </it>karyotype. The distribution of recombination frequencies and distorted transmission of parental alleles differed from those of a previous inter-species hybrid. The differences varied in magnitude and direction between chromosomes, suggesting that they had multiple causes. The map, which covered an estimated of 95% of the genome with an average interval of 2 cM, was used to analyze the distribution of a newly discovered family of MITE transposons and tested for its utility in positioning seven mutations that affect aspects of plant size.</p> <p>Conclusions</p> <p>The current map has an estimated interval of 1.28 Mb between markers. It shows a lower level of transmission ratio distortion and a longer length than the previous inter-species map, making it potentially more useful. The molecular recombination map further indicates that the <it>IDLE </it>MITE transposons are distributed throughout the genome and are relatively stable. The map proved effective in mapping classical morphological mutations of <it>A. majus</it>.</p>
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